Does a barcoding gap exist in prokaryotes? Evidences from species delimitation in cyanobacteria.

Eckert EM, Fontaneto D, Coci M, Callieri C - Life (Basel) (2014)

Bottom Line:
Nevertheless, the application of predetermined threshold in genetic distances to identify units of diversity (Operative Taxonomic Units, OTUs) may provide biased results.Here we tests for the existence of a barcoding gap in several groups of Cyanobacteria, defining units of diversity according to clear differences between within-species and among-species genetic distances in 16S rRNA.The application of a tool developed for animal DNA taxonomy, the Automatic Barcode Gap Detector (ABGD), revealed that a barcoding gap could actually be found in almost half of the datasets that we tested.

ABSTRACTThe amount of information that is available on 16S rRNA sequences for prokaryotes thanks to high-throughput sequencing could allow a better understanding of diversity. Nevertheless, the application of predetermined threshold in genetic distances to identify units of diversity (Operative Taxonomic Units, OTUs) may provide biased results. Here we tests for the existence of a barcoding gap in several groups of Cyanobacteria, defining units of diversity according to clear differences between within-species and among-species genetic distances in 16S rRNA. The application of a tool developed for animal DNA taxonomy, the Automatic Barcode Gap Detector (ABGD), revealed that a barcoding gap could actually be found in almost half of the datasets that we tested. The identification of units of diversity through this method provided results that were not compatible with those obtained with the identification of OTUs with threshold of similarity in genetic distances of 97% or 99%. The main message of our results is a call for caution in the estimate of diversity from 16S sequences only, given that different subjective choices in the method to delimit units could provide different results.

life-05-00050-f003: Rooted Maximum Likelihood phylogenetic trees for three datasets with barcoding gap presented in Figure 2. Scale bars represent the number of substitutionns per site according to the GTRMIX model. All branches depicted are supported by bootstrap values of 100%. The numbers represent unique sequences within the clade. Colors within each bar correspond to 99% identity Operative Taxonomic Units (OTUs) within the collapsed monophyletic clades and the dark grey squares represent ABGD units (AU). The names correspond to the ones from SILVA database 111 [32].

Mentions:
In order to visually compare the identification of ABGD units and OTUs, we visualized the phylogenetic reconstructions for Planktothrix, Fischerella and Arthrospira, the three genera where a barcoding gap was unambiguously found. In all three cases the ABGD units corresponded completely with monophyletic phylogenetic groups on the trees (Figure 3). In the case of the genus Planktothrix, the 99% OTUs corresponded with monophyletic groups nested within ABGD units. For example, ABGD unit 1 (AU1 in Figure 3A) consisted of three OTUs. In contrast, all ABGD units but not all OTUs resulted monophyletic in Arthrospira and Fischerella. Three OTUs in Fischerella where distributed within two different monophyletic groups corresponding to two ABGD units (Figure 3B). For Arthrospira, six OTUs were mixed within the same monophyletic group corresponding to one ABGD unit (Figure 3C).

life-05-00050-f003: Rooted Maximum Likelihood phylogenetic trees for three datasets with barcoding gap presented in Figure 2. Scale bars represent the number of substitutionns per site according to the GTRMIX model. All branches depicted are supported by bootstrap values of 100%. The numbers represent unique sequences within the clade. Colors within each bar correspond to 99% identity Operative Taxonomic Units (OTUs) within the collapsed monophyletic clades and the dark grey squares represent ABGD units (AU). The names correspond to the ones from SILVA database 111 [32].

Mentions:
In order to visually compare the identification of ABGD units and OTUs, we visualized the phylogenetic reconstructions for Planktothrix, Fischerella and Arthrospira, the three genera where a barcoding gap was unambiguously found. In all three cases the ABGD units corresponded completely with monophyletic phylogenetic groups on the trees (Figure 3). In the case of the genus Planktothrix, the 99% OTUs corresponded with monophyletic groups nested within ABGD units. For example, ABGD unit 1 (AU1 in Figure 3A) consisted of three OTUs. In contrast, all ABGD units but not all OTUs resulted monophyletic in Arthrospira and Fischerella. Three OTUs in Fischerella where distributed within two different monophyletic groups corresponding to two ABGD units (Figure 3B). For Arthrospira, six OTUs were mixed within the same monophyletic group corresponding to one ABGD unit (Figure 3C).

Bottom Line:
Nevertheless, the application of predetermined threshold in genetic distances to identify units of diversity (Operative Taxonomic Units, OTUs) may provide biased results.Here we tests for the existence of a barcoding gap in several groups of Cyanobacteria, defining units of diversity according to clear differences between within-species and among-species genetic distances in 16S rRNA.The application of a tool developed for animal DNA taxonomy, the Automatic Barcode Gap Detector (ABGD), revealed that a barcoding gap could actually be found in almost half of the datasets that we tested.

ABSTRACTThe amount of information that is available on 16S rRNA sequences for prokaryotes thanks to high-throughput sequencing could allow a better understanding of diversity. Nevertheless, the application of predetermined threshold in genetic distances to identify units of diversity (Operative Taxonomic Units, OTUs) may provide biased results. Here we tests for the existence of a barcoding gap in several groups of Cyanobacteria, defining units of diversity according to clear differences between within-species and among-species genetic distances in 16S rRNA. The application of a tool developed for animal DNA taxonomy, the Automatic Barcode Gap Detector (ABGD), revealed that a barcoding gap could actually be found in almost half of the datasets that we tested. The identification of units of diversity through this method provided results that were not compatible with those obtained with the identification of OTUs with threshold of similarity in genetic distances of 97% or 99%. The main message of our results is a call for caution in the estimate of diversity from 16S sequences only, given that different subjective choices in the method to delimit units could provide different results.